Under the Dark Sky
by Dividedwefell
Summary: AU set sometime after the first half of the season. Skye is convinced the only way to save Coulson and solve the mystery surrounding his death is to transfer teams. By leaving, the whole team thinks Skye betrayed them a second time. Yet, Skye will need her old team more than ever if she is to survive and somehow save them all. (My first attempt at writing a fanfiction).
1. Darkness Falls

_Author's Note: This story is an AU set sometime before the midwinter finale. Coulson was never taken but the Myles thing did happen. It is kind of a slow start getting everything set up.  
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_PS. I have never actually written a story before so please be patient with all of my mistakes & any constructive criticism is welcome and I will try to improve._

_Disclaimer: Don't own it. Can't even say I wish I did. Just attempting to borrow them and see how it goes. _

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_Prologu_e…

_"Look Skye, we know it was you that hacked into S.H.I.E.L.D.'s level 8 server to retrieve the information on Agents Fitz and Ward's mission," said Agent Burke. He and Agent Walkerson had caught Skye on her way to a mission briefing at the Hub and demanded she sit down and talk with them. That had been almost an hour ago and as it turned out Agent Burke was more interested in talking than listening. Agent Walkerson hadn't spoken a word since Agent Burke had finished presenting his offer. He was staring and Skye found herself starting to get annoyed with the whole situation._

_"So?" Skye questioned disbelief evident in her tone. "I've done worse before and Director Fury never felt the need to pull me off a mission to bring in the big guns for questioning. What's changed?"_

_"You have" Burke responded "when you chose to look for the files on your teammates instead of on your parents, yes Skye we know all about your search for information on your heritage. That showed remarkable loyalty to your team. It proved I was right and that you were the right kind of person for this job."_

_"As you pointed out," Skye said through gritted teeth, not entirely happy with how the SHIELD agent was carelessly throwing around her deepest secrets, "I do care about my team. I am just starting to regain their trust. Why would I let them think I had betrayed them yet again?"_

_"Because, " Burke said solemnly, "Agent Coulson didn't ever go to Tahiti. He needs you now and he doesn't even know it. So if you turn us down, you go back to the bus, rejoin the team and things will probably go back to normal, at least for a little while. But when everything does go down. And it will. You will always wonder if you could have stopped it. So what do you say Skye? You can be part of the team or you can work to keep Coulson one step ahead in the battle he doesn't even know he is fighting."_

_Skye knew she owed Coulson a lot. He had given her a second chance when no one else would. He had given her information on her parents when she certainly hadn't deserved it. That meant the world to Skye. If Coulson really did need her help, well that that was the only thing Skye could think of that would cause her to give up her new-found family to accept the agent's offer._

_"Alright, fine. I'm in."_

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Chapter One- Lights out.

It had been nearly six months since Fitz had accidentally discovered the encrypted data leaks being sent out from the Bus computers. It had taken him a week to conclusively link the activity to Skye and an additional week before he convinced himself the leaks could have no other rational explanation; at which point he brought the information to Coulson. Fitz wasn't stupid. He knew what a betrayal from Skye would do to the team, especially since they had already given her a second chance so he had waited till he was 100% sure before he brought the information forward. Even the hardened agent Ward seemed like he was finally starting to come around to the young hacker's charms. Fitz hadn't been wrong about the toll it would take. It had destroyed the team though no one would show it in the difficult months that followed.

Skye had never seen Coulson look as angry as he did the day Fitz had finally reported the planted info leaks to him. In a way she had been almost relieved. She had been waiting on this day for almost two weeks since Agent Burke had texted her and told her that things had been put in motion for her transfer. She hadn't understood why joining Burke's team or "going dark" as he often referred to it required such a drastic severing of ties with the people she considered to be her family but as weeks passed and then months she began to understand. Families didn't give up on one another and as long as she was considered a part of the team neither would they have given up on her. She was willing to hack into level 8 security to make sure Fitz and Ward made it safely home and that kind of loyalty worked both ways. That much was evidenced by FitzSimmons and how like clockwork whenever the Bus was in town the two would head down to the prison level to visit her. They were always told the same thing that Skye wasn't accepting visitors but the visits continued anyways. If those two were willing to show such loyalty to someone they fully believed to have betrayed them—twice; Skye couldn't imagine that they would have been able to accept her transfer to a department known for its highly dangerous and highly classified missions.

Granted, the last six months had been pretty light on missions and pretty heavy on training. Agent Walkerson had turned out to be her new S.O. and his training tactics made Ward seem like a teddy bear. Skye trained 7 days a week from 4 a.m. to 12 p.m. rain or shine and then the afternoon was filled with either class (which Skye hated) or gathering information from the nets (which Skye loved). Skye's marksmanship had drastically improved. She had come a long way from the young civilian who reflexively said _bang_ every time she pulled the trigger. To her surprise, Skye found that once she stopped goofing off that she was pretty good with a gun. She hadn't been at the compound long before she and everyone else at the shooting range knew she was capable of hitting what she aimed for. Skye hadn't forgotten Quinn's words and honestly wasn't sure she could pull the trigger if her target was alive but for now she kept that fear to herself. Her hand to hand had improved as well courtesy of sparring sessions with Agent Romanoff whenever the woman was at the hub. Romanoff scared Skye but she was a fantastic teacher and Skye progressed rapidly under her tutelage.

Skye now lived and operated out of the dungeon, which was what they called the lower level of the hub where all the "dark" agents slept and trained. They were considered dark; Skye learned because that is where they operated—off the grid. Dark agents didn't get loud fancy extractions or the luxury of SHIELD badges opening closed doors. Any contacts they had were their own. Dark missions were long, the sort of operation where the covers were so deep it could take weeks to get an alias in place and months before an agent was able to start feeding back any useable intel. Some of these agents had maintained the same cover for years while they worked their way up to the inner circles of various companies and governments. Skye sometimes wondered how the agents remembered their real identities after pretending to be someone else for so long. Sometimes she could relate.

No-one called her Skye anymore. No one here knew her real name besides Burke and Walkerson who could only use it when they were alone. Upon transferring, she had been forced to adopt a last name and she had become Agent Caelum to all those who addressed her by name. Yes, she was an agent now. Fury had made it official about a month after the transfer. He, Skye, Burke, and even the ever-silent Walkerson had celebrated with cheap champagne served in paper cups. Skye briefly wished that Coulson could have been there to see it and wondered if he would have been proud of her but it had been a fleeting thought. It was too hard to think of Coulson, Jemma, Fitz, May and especially Ward. She missed her burly former S.O., how he had seemed to genuinely care about her and the team and if she was being honest she missed the butterflies in her stomach she had gotten when she was around him. Agent Walkerson was more the strong silent type. It had been six months and Skye still didn't know much about him. If Skye were to be honest with herself she would admit that she still thought of Ward as her S.O., Walkerson was just a placeholder.

Much to Skye's frustration, she still hadn't been given any more information on Coulson or Tahiti. She knew he had died and been brought back but not the specifics or how her going dark was supposed to help him. She had brought it up to Agent Burke on several occasions but his answer was always the same

"Patience, Agent Caelum. You aren't on the bus anymore with their mission of the week." He always said. "Things work different down here. "

Skye couldn't disagree there.


	2. April Showers

_Author's Note: I am so sorry it took me so long to update! Instead of having more time over the holidays, I ended up having less. I will try to be more prompt in the future. I already started on chapter three at least :) Thank you all so much for reading and reviewing! I really appreciated the suggestions. By the way, this chapter doesn't have the rest of the team in it but I promise they will all be back soon if you hang in there._

_Disclaimer: Don't own it. Can't even say I wish I did. Just attempting to borrow them and see how it goes. _

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Chapter Two- April Showers

"Alright Rookie, that'll do for now. Get cleaned up. Agent Burke wants us in his office in ten." Both Walkerson and Skye were dripping sweat from their morning workout session. Skye was long past the days of complaining about every workout session but ten minutes to shower and change?

"Gee thanks for leaving me so much time" Skye retorted grabbing her gym bag and huffing her way toward the showers.

"I heard that Rookie" Walkerson called out, "next time I'm only giving you five!" It was an empty threat. Walkerson actually hadn't meant to leave so little time but he had gotten carried away with trying to push her just a little farther. He was impressed with the effort Skye put into her workouts and he had to admit the girl was turning into a fine agent. He was proud to be her S.O., though he would never admit that to her. He was aware the relationship went mostly one way. He had trained with Grant Ward and knew going in that replacing Ward wouldn't be easy but the loyalty Skye had shown toward Grant surprised even him. It wasn't in what she said as she never mentioned her old team, it was in the hard look she would get on her face every time someone referred to him and not Ward as her S.O. Walkerson tried not to let this bother him and he had almost convinced himself he would be grateful when the young agent was done with her training and out of his hair. If he had to guess (and his guesses were usually right) it wouldn't be too much longer now till she was cleared for fieldwork and soon after that she would be on her own.

As usual, Walkerson wasn't wrong. When Skye showed up at Burke's office exactly 9 minutes 59 seconds later with her hair dripping water on the floor, Burke informed them about a young girl named April Lewis who was showing signs of unusual abilities. Their mission was to retrieve the girl.

"So what?" Skye interrupted remembering why she had initially hated SHIELD in the first place. "We just bring her in? What if she doesn't want to come? Let me guess, she doesn't get a choice. Does she?"

Walkerson was confused for an entirely different reason. "Respectfully sir, retrieval duty is hardly a mission suited to our line of work. There are suits with badges upstairs for that. The rookie's old team, for one, why us?"

"Because," Burke responded "this isn't exactly your typical meet and greet scenario. April, unfortunately slipped under SHIELDS' radar so when the rising pharmaceutical company OCEANLIGHT incorporated identified her unique gifts, April wasn't on the registry to which you take so much offense, Skye. And since she wasn't on the registry, SHIELD had no reason to become involved when her mother reported that her daughter was being experimented on over a year ago. We had no reason to second-guess the police report that listed April's mother of being unstable and delusional. No reason until now that is. We got a tip off from an undercover agent that April is in fact an unwilling test subject for the company. However, if known shield agent's start poking around Oceanlight Inc. that could start investigations that end up bringing attention on our operative that we don't want."

"So" Skye interrupted, feeling a little ashamed of her previous accusations, "we have to go rescue April without them ever knowing SHIELD was involved."

"Exactly. But first, I want you to go on a little fact-finding mission and put together a profile on this April. Dig into Oceanside as well if you can but be extra careful to make sure to leave no trace. You had better be sure Oceanside is monitoring for signs they are being investigated by law enforcement or anyone else."

"You got it boss" Skye replied growing excited at the prospect of getting the mission underway. "I take it I am excused from _Intermediate Russian for spies and other people who like ugly languages_ today?" Skye burst out in one impressive mouthful. She hated the Russian professor Madam Scolov and she whined to Burke about the class every chance she got. Burke smiled at this. He was glad that Skye's efforts to mature as an agent hadn't stripped the girl of her personality. He had wanted her on the team because she had showed promise and was loyal to Coulson but it hadn't taken long before he had seen why Coulson had liked the girl so much.

"Just get out of my office Skye" Burke said with a roll of his eyes. "Oh and good luck!"

"Thanks, Agent Burke" Skye responded a smile lighting up her face. She felt confident that all her hard work was going to pay off. Soon she would be ready to help out Coulson for real.

_11 days later… _

Skye figures she must be the first agent in SHIELD history to end her first mission as an actual agent locked in a padded room on the psych floor of the base hospital. She hadn't gone insane, exactly. It's just that little things like walking the hallways or holding a conversation now seem to entail processing so much sensory information she ends up screaming her head off until she either passes out or someone sedates her. The mission had started out _so well_ too.

After leaving Burke's office, she and Walkerson had sat down to brainstorm ideas for April's extraction. For the first time, Skye saw the benefit of working with her new S.O. as he actually seemed to listen to her ideas unlike a certain former team member she tried really hard not to think about. Walkerson even admitted she had some "pretty good ideas… for a rookie".

Skye's plan had been easy to set in motion. The next afternoon Oceanside's current nighttime janitor, an elderly gentleman by the name of Frank, was scheduled for his yearly employment physical. Somewhat paradoxically, given its view on kidnapping small children, Oceanside did seem to feel passionately about maintaining employee health. As part of this maintenance, Oceanside required its employees to undergo yearly Tuberculosis screens. Frank was an immigrant who had received the BCG vaccine as a child so in lieu of traditional PPD skin test he was scheduled for a yearly X-ray, which he had gotten the day before. Oceanside contracted out employee health; so Skye was able to hack into the electronic health records system and replace Frank's films with ones indicative of active tuberculosis infection with no one in Oceanside's computer security division being the wiser. By the time Frank's appointment was over, the hospital was prepping for a new admission to the isolation ward, the CDC was preparing to contain a tuberculosis outbreak and Oceanside had a temporary opening on their evening janitorial staff.

Coincidentally, on his way to work that day the head of Oceanside's HR department blew a tire. He was already late for a very important meeting, which was very out of character because he was never late. He swore he had left on time but it had taken him forever to get to work, as he seemed to have hit every single red light between his house and the office (one of Fitz's better rainy day inventions). Now with the blown tire, he would be lucky if he didn't miss the meeting entirely. The meeting really was very important so he felt like he had no choice but to accept when Agent Walkerson told him to hail a cab and that switching the tire and bringing it to Oceanside would be his random act of kindness for the day. The man spent the next two hours convinced he would never see his car again so imagine his surprise when he saw that his car had not only been returned spare tire intact but it had been washed and waxed as well. His secretary mentioned the young savior was looking for work and so when the janitorial position opened up that day Mr. Walkerson had seemed like the natural choice.

Once inside the facility, Walkerson had two primary objectives. The first was to construct a floor map so that Skye could quickly and efficiently locate April and then the exit hopefully without encountering any opposition. He had always been a fan of the hope for the best plan for the worst mentality so his second objective was to sneak the components of a gun passed the metal detector so at the very least Skye would be armed if anything were to go wrong.

While Walkerson was busy with his new janitorial duties, Skye worked on building herself the online persona of a brilliant young chemist interested in pharmaceutical research. She then made sure that if someone was looking hard enough, say she was suspected in the theft of a research subject, that they would be able to find links between her alias and a pharmaceutical company that was a known rival of Oceanside.

Skye also began building a profile on April. Between old police records, school reports and even some interviews with former teachers and friends she was able to build a picture of precocious 8-year-old girl with an unnatural aptitude for fixing things. She caught Oceanside's interest when she made the local paper for fixing a robot that an older child had built for the school science fair. Oceanside was interested in the use of nanotechnology for increasing the efficiency of drug delivery so the rational behind their interest in April was clear. A month after the newspaper article had been published; April's mother filed the first police report detailing suspected experiments on her daughter. It appeared the company had recruited April under the guise of an after school science program for students showing promise in the sciences. According to the report, April had started coming home from the program with bruises on her arms from frequent blood draws. When April's mother wouldn't let the matter drop the police got a local psychiatrist involved who ruled the woman a "danger to herself and others" and admitted her to the state mental hospital for treatment. After that custody of April was transferred to the state and the trail went cold.

It was easy enough for Skye to gain access to Oceanside's facility. All it took was an emailed inquiry to the facility about the possibility of partnering with Oceanside's lab in a summer research project and whether or not it would be possible to arrange a tour. Skye knew that Oceanside's public relations firm would jump at the chance to _foster young minds_ or something like that and in no time at all it was all arranged.

Skye showed up for her Oceanside tour rocking what she informed Walkerson was "nerd chic" with over-sized glasses, a plaid skirt and Mary Janes. The ensemble was completed by the insertion of a new sub-dermal communication prototype that allowed her to be in constant contact with Walkerson without any fear of discovery. Skye had initially refused this addition feeling it to be too "Big Brother is watching" for her taste but Walkerson put his foot down and Skye had eventually relented.

After several hours listening being shown around endless labs that quite frankly looked the same and being forced to "ooo and ahhh" over descriptions of projects only FitzSimmons would understand it was finally time for lunch, and the first part of her plan. She parted from her tour guides with protests of needing to use the restroom and promises to meet up with them in the cafeteria when she was through. Skye needed to grab the gun Walkerson had hidden for her underneath the waste removal bag inside the middle stall the night before. "Eww Walkerson" Skye muttered, "Could you have possibly found anywhere more gross to hide this thing?" Skye didn't quite catch Walkerson's response but she was pretty sure it had something to do with being an "ungrateful rookie on a cushy assignment" and "didn't get my master's degree to work as a janitor" etc. Skye just grinned. For all his higher education, Walkerson lacked the computer skills to hack into the security video feed and erase the footage after April had been broken out leaving him stuck with the janitor role. Skye secured the gun under her skirt. Something about the feel of the gun strapped to her thigh made her feel confident and capable. She was an agent of Shield and she had a mission to complete.

After the completion of her tour, Skye dipped into a supply closet and stayed until the majority of the building was closed for the evening. She then made her way down to the lab where Walkerson thought April was being held and within 30 seconds hacked the keypad locking the door. Inside the room was a small bed, a dresser and huddled in the corner a small girl clutching a brown and caramel colored kitten. At the sight of Skye, the girl's big blue eyes widened with apprehension.

"April?" Skye started softly. "My name is Skye. I've come to take you away from here."

"Really?" April's eyes widened with hope "like to my mom?" Skye hesitated unsure how to tell the girl that her mother was being held in a mental institution but also unwilling to lie to her. April took in Skye's expression and her little face fell. Skye decided on a version of the truth.

"Honestly sweetie, the people that took you, took away your mom too. I promise we are gonna go get her too but it was more important to get you first. Does that make sense?" April nodded solemnly.

"Okay. Well can Snickers come?" she asked holding up her cat. "I found her and she will be all alone if we leave her."

"Of course Snickers can come," Skye smiled. "No one gets left behind. But we really need to hurry and I really need you to stay as quiet as you can." April smiled and nodded, shifting the kitten so she held it with one-hand, she placed her other hand in Skye's.

What Skye didn't anticipate was that after erasing the video footage of her and April; she would run into another scientist on their way out of the building. She definitely didn't expect that this scientist would decide to use a syringe, which was filled with an experimental serum designed to enhance one's natural abilities as a weapon. Skye felt the needle pierce her skin, the sting of the serum as it was injected and the terrible whole body burning sensation that followed it. She could hear April crying out for her and the sound gave Skye the strength to fight off the scientist and lead them to the exit and the waiting Walkerson.

It was only once she was in the van with Walkerson that Skye was able to see past the painful burning sensation and begin to process—everything. She could see and hear everything; the sound of the seat belt rubbing against April's shirt, of Walkerson's voice, of the wheels turning against the pavement. It was too much. Pressure was building in her head and Skye could hear a horrible wailing sound she eventually realized was her own screams. The pain and the sensations built more and more until mercifully, everything went black.


End file.
